I would like to use proteins for my weavile, but when i trained it from egg, i use exp. share with him, so is that exp.share changed the EVs point, since the protein and another medicine like that only work if the EV total point is under 100 point
If you used Exp Share while training you would still have gained EVs. You gain the same EVs that the main battler got.
And once you get to 100 EVs you cannot use vitamins any more.